In flowering plants, successful germinal cell development and meiotic recombination depend upon a combination of environmental and genetic factors. To gain insights into this specialized reproductive development program we used short- and long-read RNA-sequencing (RNA-seq) to study the temporal dynamics of transcript abundance in immuno-cytologically staged barley (Hordeum vulgare) anthers and meiocytes. We show that the most significant transcriptional changes in anthers occur at the transition from pre-meiosis to leptotene–zygotene, which is followed by increasingly stable transcript abundance throughout prophase I into metaphase I–tetrad. Our analysis reveals that the pre-meiotic anthers are enriched in long non-coding RNAs (lncRNAs) and that entry to meiosis is characterized by their robust and significant down regulation. Intriguingly, only 24% of a collection of putative meiotic gene orthologs showed differential transcript abundance in at least one stage or tissue comparison. Argonautes, E3 ubiquitin ligases, and lys48 specific de-ubiquitinating enzymes were enriched in prophase I meiocyte samples. These developmental, time-resolved transcriptomes demonstrate remarkable stability in transcript abundance in meiocytes throughout prophase I after the initial and substantial reprogramming at meiosis entry and the complexity of the regulatory networks involved in early meiotic processes.

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12Pasteuria penetrans is a gram-positive endospore forming bacterial parasite of Meloidogyne spp. the 13 most economically damaging genus of plant parasitic nematodes globally. The obligate antagonistic 14 nature of P. penetrans makes it an attractive candidate biological control agent. However, deployment 15 of P. penetrans for this purpose is inhibited by a lack of understanding of its metabolism and the 16 molecular mechanics underpinning parasitism of the host, in particular the initial attachment of the 17 endospore to the nematode cuticle. Several attempts to assemble the genomes of species within this 18 genus have been unsuccessful. Primarily this is due to the obligate parasitic nature of the bacterium 19which makes obtaining genomic DNA of sufficient quantity and quality which is free from 20 contamination challenging. Taking advantage of recent developments in whole genome amplification, 21 long read sequencing platforms, and assembly algorithms, we have developed a protocol to generate 22 large quantities of high molecular weight genomic DNA from a small number of purified endospores. 23We demonstrate this method via genomic assembly of P. penetrans. This assembly reveals a reduced 24 genome of 2.64Mbp estimated to represent 86% of the complete sequence; its reduced metabolism 25 reflects widespread reliance on the host and possibly associated organisms. Additionally, apparent 26 expansion of transposases and prediction of partial competence pathways suggest a high degree of 27 genomic plasticity. Phylogenetic analysis places our sequence within the Bacilli, and most closely 28 related to Thermoactinomyces species. Seventeen predicted BclA-like proteins are identified which 29 may be involved in the determination of attachment specificity. This resource may be used to develop 30 in vitro culture methods and to investigate the genetic and molecular basis of attachment specificity. 31 32 33

In flowering plants, successful germinal cell development and meiotic recombination depend upon a combination of environmental and genetic factors. To gain insights into this specialised reproductive development programme we used short- and long-read RNA-sequencing (RNA-seq) to study the temporal dynamics of transcript abundance in immuno-cytologically staged barley (Hordeum vulgare) anthers and meiocytes. We show that the most significant transcriptional changes occur at the transition from pre-meiosis to leptotene–zygotene, which is followed by largely stable transcript abundance throughout prophase I. Our analysis reveals that the developing anthers and meiocytes are enriched in long non-coding RNAs (lncRNAs) and that entry to meiosis is characterized by their robust and significant down regulation. Intriguingly, only 24% of a collection of putative meiotic gene orthologues showed differential transcript abundance in at least one stage or tissue comparison. Changes in the abundance of numerous transcription factors, representatives of the small RNA processing machinery, and post-translational modification pathways highlight the complexity of the regulatory networks involved. These developmental, time-resolved, and dynamic transcriptomes increase our understanding of anther and meiocyte development and will help guide future research.One sentence summaryAnalysis of RNA-seq data from meiotically staged barley anthers and meiocytes highlights the role of lncRNAs within a complex network of transcriptional and post-transcriptional regulation accompanied by a hiatus in differential gene expression during prophase I.The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Robbie Waugh (robbie.waugh@hutton.ac.uk)